MolNFT v1 · #55457 · protein
Structural determinants of the beta-selectivity of a bacterial aminotransferase
2YKY · Beta-transaminase: “Structural determinants of the beta-selectivity of a bacterial aminotransferase”. X-ray diffraction, 3 ligands (SFE, PLP, BNZ), 12 pockets (best druggability 0.78). MolNFT v1 #55457 on GenesisL1: 3D structure…
- PDB
- 2YKY
- Type
- protein
- Length
- 1,291 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-transaminase
- UniProt
- A3EYF7
- Ligands
- SFE, PLP, BNZ
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-transaminase | protein | 431 | 48% helix, 17% strand | A3EYF7 |
| B | Beta-transaminase | protein | 429 | 48% helix, 17% strand | A3EYF7 |
Ligands and binding sites
- SFE · (3S)-3-amino-3-phenylpropanoic acid · ligand · 4 copies · chains A, B, C
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- BNZ · Benzene · ligand · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.78 | 0.98 | 40 | EDO |
| 2 | 745 | 0.75 | 0.80 | 67 | PLP, SFE |
| 3 | 657 | 0.74 | 0.80 | 65 | PLP, SFE, EDO |
| 4 | 524 | 0.71 | 0.80 | 47 | GOL |
| 5 | 264 | 0.58 | 0.78 | 33 | PLP, SFE |
Interfaces
3 interfaces between chains.
- A–B · 4519 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 371 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 93 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YKY · Structural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A3EYF7
- Elsewhere: RCSB PDB 2YKY · PDBe 2YKY · UniProt A3EYF7
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